The 77th-minute incursion briefly halted the game after Ryan Ledson and Alan Browne had given Preston a clear advantage before substitute Lukas Jutkiewicz's late consolation.
There was also a banner unfurled in front of the directors' box saying '#BSHL Out' in reference to owners Birmingham Sporting Holdings Limited.
The Blues could now face action from the Football Association over the pitch invasion, which came after a group protested against the club's absent owners, chanting: "You faceless b******s, get out of our club".
Blues have now lost five Championship games in a row and Eustace acknowledged the fans' frustrations but wants them to stick with the team.
"Up until four or five games ago the fans and the players have been connected and it's been very tight, something we've built over a period of time," said Eustace.
"It's important we get back to that. The most important thing for me is the fans are proud to support this team.
"We just need to get back to what we were doing and make sure these fans - no matter what's going on around the club - get back to looking after the boys.
"In the second half, the fans did keep with us and we could have maybe nicked an equaliser in the end.
"But we need the fans to stay with the team."
Preston effectively won the game in the first 15 minutes.
Midfielder Ledson drove home a loose ball from the edge of the box after Blues missed the chance to clear Robbie Brady's cross in the 10th minute.
Browne quickly doubled their lead by heading home Brady's near-post corner.
Jutkiewicz headed home in the 83rd minute to meet Maxime Colin's cross but Preston held on.
Eustace admitted: "The manner we conceded the goals were very soft - we had a number of chances to clear the ball and we didn't pick up from the set-piece."